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| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-01-29 10:35:52 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-01-30 10:45:27 +0100 |
| commit | 241e122193e6eee900cab1f3a1caec2f90603560 (patch) | |
| tree | 728f0046a3d103ea7abd9739bc16b2326d68b190 | |
| parent | e89fa047f76048ac907756a5f08ddc06c84c6c40 (diff) | |
| download | guix-241e122193e6eee900cab1f3a1caec2f90603560.tar guix-241e122193e6eee900cab1f3a1caec2f90603560.tar.gz | |
gnu: bowtie: fix build errors
* gnu/packages/bioinformatics.scm (bowtie): Add 'supported-systems' field and
add Makefile patch.
* gnu/packages/patches/bowtie-fix-makefile.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
| -rw-r--r-- | gnu-system.am | 1 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 6 | ||||
| -rw-r--r-- | gnu/packages/patches/bowtie-fix-makefile.patch | 31 |
3 files changed, 36 insertions, 2 deletions
diff --git a/gnu-system.am b/gnu-system.am index 6c2d66bbda..1211855f54 100644 --- a/gnu-system.am +++ b/gnu-system.am @@ -346,6 +346,7 @@ dist_patch_DATA = \ gnu/packages/patches/automake-skip-amhello-tests.patch \ gnu/packages/patches/avahi-localstatedir.patch \ gnu/packages/patches/avrdude-fix-libusb.patch \ + gnu/packages/patches/bowtie-fix-makefile.patch \ gnu/packages/patches/bigloo-gc-shebangs.patch \ gnu/packages/patches/binutils-ld-new-dtags.patch \ gnu/packages/patches/binutils-loongson-workaround.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ff6c3379af..620c8090b7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2014 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2014, 2015 Ricardo Wurmus <rekado@elephly.net> ;;; ;;; This file is part of GNU Guix. ;;; @@ -95,7 +95,8 @@ BED, GFF/GTF, VCF.") (("^CPP = .*$") "CPP = g++") ;; replace BUILD_HOST and BUILD_TIME for deterministic build (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"") - (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))))) + (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))) + (patches (list (search-patch "bowtie-fix-makefile.patch"))))) (build-system gnu-build-system) (inputs `(("perl" ,perl) ("perl-clone" ,perl-clone) @@ -133,6 +134,7 @@ aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.") + (supported-systems '("x86_64-linux")) (license license:gpl3+))) (define-public samtools diff --git a/gnu/packages/patches/bowtie-fix-makefile.patch b/gnu/packages/patches/bowtie-fix-makefile.patch new file mode 100644 index 0000000000..5ac65731cb --- /dev/null +++ b/gnu/packages/patches/bowtie-fix-makefile.patch @@ -0,0 +1,31 @@ +From 4a99b0023bdfbbe486b9649489a32ea184c18c9a Mon Sep 17 00:00:00 2001 +From: Valentin Antonescu <valentin@jhu.edu> +Date: Tue, 2 Dec 2014 11:19:13 -0500 +Subject: [PATCH] Make sure the Mavericks test happens only under Darwin. + +--- + Makefile | 11 +++++------ + 1 file changed, 5 insertions(+), 6 deletions(-) + +diff --git a/Makefile b/Makefile +index d74f7c8..a4cdfa7 100644 +--- a/Makefile ++++ b/Makefile +@@ -54,12 +54,11 @@ endif + MACOS = 0 + ifneq (,$(findstring Darwin,$(shell uname))) + MACOS = 1 +-endif +- +-ifneq (,$(findstring 13,$(shell uname -r))) +- CPP = clang++ +- CC = clang +- EXTRA_FLAGS += -stdlib=libstdc++ ++ ifneq (,$(findstring 13,$(shell uname -r))) ++ CPP = clang++ ++ CC = clang ++ EXTRA_FLAGS += -stdlib=libstdc++ ++ endif + endif + + POPCNT_CAPABILITY ?= 1 |